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I added a setting to the Taxonomy Manager to disable the overwriting of the taxonomy/term/% path by the Taxonomy Manager. The hook_menu_alter is used to redirect terms selected in the merging feature (which get deleted afterwards) to the resulting merged term, so this redirect feature is not essential for the Taxonomy Manager and users can now decide whether to active it or not.

Hey I added the new 6-2x-dev version and I don't see the switch to turn off the overriding of taxonomy/%term/ page on the taxonomy manager module admin page. Can you please tell me where the menu item is?

Okay, found it, thanks...I didn't notice that secondary management menu...but it disables the redirect of merged terms...but it doesen't seem to disable the override of the taxonomy/%term page, which I have running through panels. I want to use taxonomy manager just to manage my taxonomy terms in an efficient fashion, I don't want it to have anything to do with my taxonomy/%term url links. How do I prevent it from overriding that page?